• Communications for Statistical Applications and Methods
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• v.29 no.1
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• pp.65-83
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• 2022

Although various statistical methods have been developed to map time-dependent genetic factors, most identified genetic variants can explain only a small portion of the estimated genetic variation in longitudinal traits. Gene-gene and gene-time/environment interactions are known to be important putative sources of the missing heritability. However, mapping epistatic gene-gene interactions is extremely difficult due to the very large parameter spaces for models containing such interactions. In this paper, we develop a Gaussian process (GP) based nonparametric Bayesian variable selection method for longitudinal data. It maps multiple genetic markers without restricting to pairwise interactions. Rather than modeling each main and interaction term explicitly, the GP model measures the importance of each marker, regardless of whether it is mostly due to a main effect or some interaction effect(s), via an unspecified function. To improve the flexibility of the GP model, we propose a novel grid-based method for the within-subject dependence structure. The proposed method can accurately approximate complex covariance structures. The dimension of the covariance matrix depends only on the number of fixed grid points although each subject may have different numbers of measurements at different time points. The deviance information criterion (DIC) and the Bayesian predictive information criterion (BPIC) are proposed for selecting an optimal number of grid points. To efficiently draw posterior samples, we combine a hybrid Monte Carlo method with a partially collapsed Gibbs (PCG) sampler. We apply the proposed GP model to a mouse dataset on age-related body weight.

• Proceedings of the Korean Society of Veterinary Pathology Conference
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• 2000.09a
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• pp.19-19
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• 2000

Most renal diseases progress by consecutive cell responses such as hypertrophy, hyperplsia, proliferation, defferentiation, sclerosis, fibrosis and other cellular degenerative process. These cellular responses are mediated by the activation of various mitogens such as vasoconstrictors, growth factors, hormone, genotoxins and cytokines through mechanical, hemodynamic, immunological injury as well as metabolic abnormality. (omitted)

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.215-220
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• 1991

MudJ(Km.lac) operon fusions were used in the identification of osmotic-inducible genetic(osi) loci in Salmonella typhimurium. Expression of osi::lacZ(osi5001, 5027) genes were dramatically induced 39-189 fold when the osmolarity was increased. Seven osm::lacZ genes were constituvely expressed under both low and high osmotic strength. The osi5001::lacZ fusion strains showed the enhanced osmotolerance and the reduced expression of the osi5001::lacZ in the presence of 1mM proline or betaine as osmoprotectants. Four osmotic inducible genetic loci were mapped into 36 (YK531), 44 (YK504), 57 (YK501) and 84 (YK528) map unit by testing the cotransduction frequency.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.3
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• pp.302-306
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• 2001

This study was carried out to construct mapping population and to evaluate the methods involved, including polymorphic DNA marker system and appropriate statistical analysis. As an initial step to establish chicken genome mapping project, White Leghorn (WL) and Korean Ogol chicken (KOC) were used for generating backcross population. From 8 initial parents, total 280 backcross progenies were obtained and 40 were used for genotyping and linkage analysis. For development of novel polymorphic markers for KOC, Random Amplified Polymorphic DNA (RAPD) markers specific for this chicken line were generated. Also included in this study were six microsatellite markers from East Lansing map as reference loci. For segregation analysis, 15 RAPD markers and 6 microsatellites were used to genotype the backcross population. Among the RAPD markers that we developed, 2 pairs of markers were identified to be linked and another 4 RAPD markers showed linkage with microsatellites of known map. In summary, this study showed that our backcross population generated from the mating of KOC to WL serves as a valuable genetic resource for genotyping. Furthermore, RAPD markers are proved to be valuable in linkage mapping analysis.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2001.10a
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• pp.14-17
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• 2001

Positional clonging (map-based cloning) of mutations or genetic variations has been served as an invaluable tool to understand in-vivo functions of genes and to identify molecular components underlying phenotypes of interest. Mice homozygous for the cerebellar deficient folia (cdf) mutation are ataxic, with cerebellar hypoplasia and abnormal lobulation of the cerebellum. In the cdf mutant cerebellum approximately 40% of Purkinje cells are ectopically located within the white matter and the inner granule cell layer (IGL). To identify the cdf gene, a high-resolution genetic map for the cdf-gene-encompassing region was constructed using 1997 F2 mice generated from C3H/HeSnJ-cdf/cdf and CAST/Ei intercross. The cdf gene showed complete linkage disequilibrium with three tightly linked markers D6Mit208, D6Mit359, and D6Mit225. A contig using YAC, BAC, and P1 clones was constructed for the cdf critical region to identify the gene. A deletion in the cdf critical region on chromosome 6 that removes approximately 150 kb of DNA selection. cdf mutant mice with the transgenic copy of the identified gene restored the brain abnormalities of the mutant mice. The positional cloning of cdf gene provides a good example showing the identification of a gene could lead to finding a new component of important molecular pathways.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.117-117
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• 2017

The onion (Allium cepa L.) is the most widely cultivated species of the genus Allium, especially it has been valued because of the pungent flavor and aroma. Allium species including onion has very large genome sizes ranging from approximately 10 to 20 Gbp, which have complicated genomic studies and precluded genome sequencing until recently. A population of 186 F2 individuals derived from a cross of 'Umjinara' ${\times}$ 'Sinsunhwang' and the two parental lines were used for this study. For the development of framework map, various types of markers including SSRs, RAPD, SNPs, and CAPS makers have been used for polymorphism test. Especially, a lot of SNP and CAPS loci were developed from the onion transcriptome sequence by RNASEQ of two parental lines. The GBS libraries have been constructed based on a modified protocol from Poland Lab using a two-enzyme system. We have been developing markers showing polymorphism between two parental lines, and genotyping for all F2 individuals were finished for a number of polymorphic markers. For the construction of GBS libraries, a set of 192 barcoded adapters were generated from complementary oligonucleotides with XhoI overhang sequence and unique barcodes of length 4-8 bp and they have been tested using two parental linesto determine the optimum conditions for GBS analysis.

• Proceedings of the KSAR Conference
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• 2001.10a
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• pp.14-17
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• 2001

Positional cloning (map-based cloning) of mutations or genetic variations has been served as an invaluable tool to understand in-vivo functions of genes and to identify molecular components underlying phenotypes of interest. Mice homozygous for the cerebellar deficient folia (cdf) mutation are ataxic, with cerebellar hypoplasia and abnormal lobulation of the cerebellum. In the cdf mutant cerebellum approximately 40% of Purkinje cells are ectopically located within the white matter and the inner granule cell layer (IGL). To identify the cdf gene, a high-resolution genetic map for the cdf-gene-encompassing region was constructed using 1997 F2 mice generated from C3H/HeSnJ-cdf/cdf and CAST/Ei intercross. The cdf gene showed complete linkage disequilibrium with three tightly linked markers D6Mit208, D6Mit359, and D6Mit225. A contig using YAC, BAC, and P1 clones was constructed for the cdf critical region to identify the gene. A deletion in the cdf critical region on chromosome 6 that removes approximately 150kb of DNA was identified. A gene associated with this deletion was identified using cDNA selection. cdf mutant mice with the transgenic copy of the identified gene restored the brain abnormalities of the mutant mice. The positional cloning of cdf gene provides a good example showing the identification of a gene could lead to finding a new component of important molecular pathways.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.5
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• pp.556-561
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• 2006

It is very important to classify the DNA Chip image pattern in order to acquire useful information about genetic disease of people. In this paper, we developed the novel pattern classification method of DNA Chip image using MLP based back-propagation and Self organizing Map learning algorithm. And then we compared and analyzed these classified pattern results. Also we carried out experiment in the MV2440 board using CPU Cote for S3C2440(ARM 920T) and PC environment, and displayed its results in order to give the genetic information to user mote easily in various environment.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.77-86
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• 2015

Chicken is one of the major livestock, especially for supplying proteins to human. The chicken genome size is approximately one-third compared with that of the human genome and regarded as a valuable model animal for genetics and development biology. In this study, we constructed the genetic linkage map for Korean native chicken (KNC) using 131 microsatellite (MS) and 8 single nucleotide polymorphism (SNP) markers. As a result, the total map length was calculated as 2729.4 cM and the average genetic distance between markers was 19.64 cM. The marker orders and genetic distances were well matched with the consensus linkage map except for the physical order of ADL0278 and MCW0351 in GGA8. In addition, the recombination rates in marcrochromosomes were 3.7 times higher than that of microchromosomes. The average numbers of alleles, expected heterozygosity (Hexp) and polymorphic information content (PIC) values were calculated as 5.5, 0.63 and 0.58, respectively. These results will give useful information for the understanding of genetic structure and QTL studies in KNC.

• Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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• v.31 no.1
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• pp.1-9
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• 2013

This paper proposes a matching algorithm to find corresponding polygon feature sets between heterogeneous digital maps. The algorithm finds corresponding sets in terms of optimizing their shape similarities based on the assumption that the feature sets describing the same entities in the real world are represented in similar shapes. Then, by using a binary code, it is represented that a polygon feature is chosen for constituting a corresponding set or not. These codes are combined into a binary string as a candidate solution of the matching problem. Starting from initial candidate solutions, a genetic algorithm iteratively optimizes the candidate solutions until it meets a termination condition. Finally, it presents the solution with the highest similarity. The proposed method is applied for the topographical and cadastral maps of an urban region in Suwon, Korea to find corresponding polygon feature sets for block areas, and the results show its feasibility. The results were assessed with manual detection results, and showed overall accuracy of 0.946.